The structure of cyclin-dependent kinase 5 (CDK5) in complex with P25 and compound 24

Structure

x-ray diffraction · 4 distinct chains · 46% helix, 11% strand (DSSP).

Ligands and binding sites

• 61U · 5-fluoranyl-4-[[2-[(1R)-1-(1-methylpiperidin-4-yl)-1-oxidanyl-ethyl]-1,6-naphthyridin-7-yl]amino]-2-morpholin-4-yl-benzenecarbonitrile · ligand · chains A
• CL · Chloride ion · ion · 19 copies · chains A, C
• EDO · 1,2-ethanediol · additive · 20 copies · chains A, B, C
• GOL · Glycerol · additive · 8 copies · chains A, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–C · 1506 Ų buried · 13 hydrogen bonds · protein-protein
• B–D · 1397 Ų buried · 14 hydrogen bonds · protein-protein
• A–B · 1224 Ų buried · 21 hydrogen bonds · protein-protein

Compared structures

• 7VDS · The structure of cyclin-dependent kinase 5 (CDK5) in complex with p25 and Compound 24 · the same entry in another collection · chain D against D, TM-score 1.00
• Q15078 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 5 activator 1 (Q15078) · a predicted model of the same protein · chain C against A, TM-score 1.00
• Q00535 · AlphaFold monomer V2.0 prediction for cyclin-dependent-like kinase 5 (Q00535) · a predicted model of the same protein · chain B against A, TM-score 0.98

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt Q00535
• Every structure of UniProt Q15078
• Elsewhere: RCSB PDB 7VDS · PDBe 7VDS · UniProt Q00535 · UniProt Q15078